SLRfinder: A method to detect candidate sex‐linked regions with linkage disequilibrium clustering DOI Creative Commons
Xueling Yi, Petri Kemppainen, Juha Merilä

et al.

Molecular Ecology Resources, Journal Year: 2024, Volume and Issue: 24(6)

Published: June 8, 2024

Despite their critical roles in genetic sex determination, chromosomes remain unknown many non-model organisms, especially those having recently evolved sex-linked regions (SLRs). These evolutionarily young and labile are important for understanding early chromosome evolution but difficult to identify due the lack of Y/W degeneration SLRs limited small genomic regions. Here, we present SLRfinder, a method candidate using linkage disequilibrium (LD) clustering, heterozygosity divergence. SLRfinder does not rely on specific sequencing methods or type reference genome (e.g., from homomorphic sex). In addition, input require phenotypic sexes, which may be population sampling, information can incorporated is necessary validate SLRs. We tested various published datasets compared it local principal component analysis (PCA) depth-based Sex Assignment Through Coverage (SATC). As expected, PCA could used SATC works better conserved chromosomes, whereas outperforms analysing when harbour inversions. Power analyses showed that worked sampling more populations share same SLR. If one population, relatively larger sample size (around 50) needed sufficient statistical power detect significant SLR candidates, although true likely always top-ranked. provides novel complementary approach identifying uncovering additional diversity nature.

Language: Английский

Diversity and Convergence of Sex-Determination Mechanisms in Teleost Fish DOI Creative Commons
Jun Kitano, Satoshi Ansai, Yusuke Takehana

et al.

Annual Review of Animal Biosciences, Journal Year: 2023, Volume and Issue: 12(1), P. 233 - 259

Published: Oct. 20, 2023

Sexual reproduction is prevalent across diverse taxa. However, sex-determination mechanisms are so that even closely related species often differ in systems. Teleost fish a taxonomic group with frequent turnovers of sex-determining and thus provides us great opportunities to investigate the molecular evolutionary underlying turnover Here, we compile recent studies on diversity fish. We demonstrate genes TGF-β signaling pathway frequently used for master (MSD) genes. MSD arise via two main mechanisms, duplication-and-transposition allelic mutations, few exceptions. also temperature influences sex determination many species, those chromosomes, higher temperatures inducing differentiation into males most cases. Finally, review theoretical models discuss what questions remain elusive.

Language: Английский

Citations

41
Introgression dynamics of sex-linked chromosomal inversions shape the Malawi cichlid adaptive radiation DOI Creative Commons
Moritz Blumer, Valentina Burskaia, I. V. Artyushin

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: July 29, 2024

Abstract Chromosomal inversions contribute to adaptive speciation by linking co-adapted alleles. Querying 1,375 genomes of the species-rich Malawi cichlid fish radiation, we discovered five large segregating in benthic subradiation that each suppress recombination over more than half a chromosome. Two were transferred from deepwater pelagic Diplotaxodon via admixture, while others established early deep clade. Introgression haplotypes lineages inside and outside radiation coincided with bursts species diversification. Inversions show evidence for transient sex linkage striking excess protein changing substitutions points towards selection on neuro-sensory, physiological reproductive genes. We conclude repeated interplay between depth adaptation sex-specific has been central evolution this iconic system.

Language: Английский

Citations

8
Sex chromosome turnover in hybridizing stickleback lineages DOI Creative Commons
Xueling Yi, Dandan Wang, Kerry Reid

et al.

Evolution Letters, Journal Year: 2024, Volume and Issue: 8(5), P. 658 - 668

Published: April 19, 2024

Recent discoveries of sex chromosome diversity across the tree life have challenged canonical model conserved evolution and evoked new theories on labile chromosomes that maintain less differentiation undergo frequent turnover. However, lack direct empirical support due to paucity case studies demonstrating ongoing turnover in nature. Two divergent lineages (viz. WL & EL) nine-spined sticklebacks (

Language: Английский

Citations

5
Yes, polygenic sex determination is a thing! DOI
Thomas D. Kocher, Richard P. Meisel, Tony Gamble

et al.

Trends in Genetics, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 1, 2024

Language: Английский

Citations

2
Evolution of Size‐Fecundity Relationship in Medaka Fish From Different Latitudes DOI Creative Commons
Shingo Fujimoto, Bayu K. A. Sumarto, Iki Murase

et al.

Molecular Ecology, Journal Year: 2024, Volume and Issue: 33(23)

Published: Nov. 5, 2024

ABSTRACT In most fishes, the number of offspring increases with maternal body size. Although this size‐fecundity relationship often varies among species as a result coevolution life‐history traits, genetic basis such relationships remains unclear. We explored underlying in two small medaka species, Oryzias latipes and O. sakaizumii . Our findings showed that has higher fecundity than , quantitative trait locus analysis using interspecific F 2 hybrids chromosome 23 is linked to relationship. particular, genes igf1 lep‐b region are known be associated including somatic growth, gonad maturation, progeny numbers various taxa. Because distributed at latitudes shorter spawning season wild, we propose relatively high observed an adaptation latitudes. also discuss potential ecological ramifications evolution increased species.

Language: Английский

Citations

1
SLRfinder: a method to detect candidate sex-linked regions with linkage disequilibrium clustering DOI Creative Commons
Xueling Yi, Petri Kemppainen, Juha Merilä

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: March 14, 2024

Abstract Despite their critical roles in genetic sex determination, chromosomes remain unknown many non-model organisms. In contrast to conserved mammals and birds, studies of fish, amphibians, reptiles have found highly labile with newly evolved sex-linked regions (SLRs). These are important for understanding early chromosome evolution but difficult identify due the lack Y/W degeneration SLRs limited small genomic regions. Here we present SLRfinder, a method candidate using linkage disequilibrium (LD) clustering, patterns heterozygosity, divergence. SLRfinder does not rely on specific sequencing methods or reference genomes require phenotypic sexes which may be from population sampling, although information can incorporated provide additional inference SLRs. We tested various published datasets compared it SATC, that identifies based depth coverage also sex. Results show SATC works better (e.g., African leopards), whereas outperforms analyzing nine-spined sticklebacks chum salmon). Since primarily relies LD clusters, is expected most sensitive harboring structural variants inversion) strongly reduced recombination rates heterozygotes. provides novel complementary approach identifying uncovering diversity nature.

Language: Английский

Citations

0
SLRfinder: A method to detect candidate sex‐linked regions with linkage disequilibrium clustering DOI Creative Commons
Xueling Yi, Petri Kemppainen, Juha Merilä

et al.

Molecular Ecology Resources, Journal Year: 2024, Volume and Issue: 24(6)

Published: June 8, 2024

Despite their critical roles in genetic sex determination, chromosomes remain unknown many non-model organisms, especially those having recently evolved sex-linked regions (SLRs). These evolutionarily young and labile are important for understanding early chromosome evolution but difficult to identify due the lack of Y/W degeneration SLRs limited small genomic regions. Here, we present SLRfinder, a method candidate using linkage disequilibrium (LD) clustering, heterozygosity divergence. SLRfinder does not rely on specific sequencing methods or type reference genome (e.g., from homomorphic sex). In addition, input require phenotypic sexes, which may be population sampling, information can incorporated is necessary validate SLRs. We tested various published datasets compared it local principal component analysis (PCA) depth-based Sex Assignment Through Coverage (SATC). As expected, PCA could used SATC works better conserved chromosomes, whereas outperforms analysing when harbour inversions. Power analyses showed that worked sampling more populations share same SLR. If one population, relatively larger sample size (around 50) needed sufficient statistical power detect significant SLR candidates, although true likely always top-ranked. provides novel complementary approach identifying uncovering additional diversity nature.

Language: Английский

Citations

0